2XCI | pdb_00002xci

Membrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, substrate-free form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5		HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND RESERVOIR (100 MM TRIS-HCL, PH 8.5, 35-40% (V/V) PEG 400, 200 MM NA-CITRATE, 50 MM 2-MERCAPTOETHANOL)

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.5	α = 90
b = 45.82	β = 97.23
c = 144.07	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH		2008-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3		MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	29.85	98.9	0.04	14.8	3.6		115974		2	37.72

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	96.7		0.55	2.2	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	NONE	2	29.854	1.36	115974	5821	98.89	0.2095	0.2071	0.2034	0.2539	0.2493

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-5.3208		-0.5529	19.052		-13.7312

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.08
f_angle_d	1.12
f_chiral_restr	0.078
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11499
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	110

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
autoSHARP	phasing